What could have happened: The Eye
by johnliz4ever
Summary: My idea about what could have happened. JohnLiz.
1. Chapter 1

Disclaimer: Don't own Stargate Atlantis, although I do dream of owning John, Aiden and Elizabeth, it would be so much fun.

Note: This contains **SPOILERS **for **'THE EYE'. **I highly recommend that if you haven't seen that episode you should turn back **NOW. **

This is my take on what could have happened if John and Aiden didn't get to Elizabeth and Rodney in time.

Pairing: Okay this is were it gets weird. Sheppard/Weir. McKay/Weir **Friendship, **Sheppard/Ford **Friendship **and somewhat bizarrely Weir/Kolya. I promise it will make sense.

**Atlantis**

Elizabeth looked at Kolya

"Are you really going to sacrifice the lives of all your men on the off chance that this city won't be completely destroyed?"

Koyla thought for a moment.

"Open the Stargate, start evacuating the remaining men."

McKay, looking relived, started to activate the Stargate.

Elizabeth turned to Kolya.

"You're making the right decision"

"You're coming with us."

Elizabeth looked at him in disbelief.

"What?"

"You'll both serve the Genii as payment for what you've done"

McKay looked at him

"For what _we've_ done?"

Two men grabbed McKay and another grabbed Elizabeth. They began to walk them down the stairs; both had guns to their backs.

"Seriously this is a bad idea! You saw what happened to my last plan; this is not what you want to do."

Koyla's men pushed McKay through the event horizon.

Elizabeth turned to Koyla

"Do you really think this is the best thing to do, Major Sheppard will come after us."

"When and if he does, he will die for what he has done to our people and you will be made to watch."

Kolya shoved Elizabeth through the event horizon just as John and Ford came into the control room. John ran to the Stargate but it shut down before he could reach it.

"Damn it."

Ford came to his side

"Sir, we need to get up to the control room now and activate the shield."

Ford looks at John and sees he is unresponsive.

"_Sir_, you want to help her, first we need to save the city"

Ford grabbed John's arm and dragged him up to the control room. Ford sat at McKay's computer and began to input the necessary information.

"2 and a half minutes till the storm hits Sir. Beckett and Teyla are still out there"

John activated his radio

"Teyla, Beckett fall back to the control room."

The two of them waited. The seconds passed, each knew that with each passing second the storm was getting closer to the city. After what seemed like an eternity Teyla and Sora walked in, supporting a barely conscious Beckett between them

"Activating shields now."

Ford hit a button, which began to charge up the shield generators. Ford looked at the control panel anxiously.

"Now"

The shield activated just in time to block the path of the wave, which was heading to the city.

Teyla looked around the group.

"Where are Dr Weir and Dr McKay?"

John looked at her and for the first time realised that Sora was in the room.

John, with an anger that came from nowhere, pushed Sora against a wall and held her by her neck choking the life out of her.

"Was this part of the plan? To take Elizabeth and McKay?"

Sora began to cough as she began to lose her battle to breath.

Ford grabbed the hand that held Sora's neck and pulls it back.

"Sir."

John reluctantly pulled his arm back and Sora slid down the wall coughing.

"It was never part of the plan; we came for the Wraith data device, the C-4 and the medical supplies, that's all. It was Kolya who decided to seize the city."

Teyla bent down next to Sora.

"Where would he have taken Dr Weir and Dr McKay?"

Sora looked around, reluctant to reveal anything, until she saw the look on John's face. The look told her that if she wants to live she should start co-operating.

"Properly home, although they will be waiting for you. If you try to rescue them they kill them…and you."

**Genii Home World **_(Several hours later)_

Elizabeth opened her eyes; her vision was blurry and she was unable to make out anything except for the bright light that was in the room.

"Elizabeth? Elizabeth can you hear me?"

Elizabeth winced.

"John?"

"Elizabeth it's Rodney."

Elizabeth opened her eyes fully and saw Rodney sat beside her. Elizabeth began to sit up and Rodney helped her. For the first time Elizabeth began to notice the pain in her ribs.

"Where are we? What happened?"

Rodney helped Elizabeth rest her back on the wall and she rested her head against his shoulder.

"I think were on the Genii home world, some sort of prison from what I can make out"

Elizabeth nodded

"How long have I been out?"

"Couple of hours."

Elizabeth sighed

"Any idea what they'll do to us?"

McKay sighed

"Don't think we want to know"

Elizabeth asked the question that was on both their minds.

"Do you think…they managed to raise the shield over Atlantis?"

McKay looked at her.

"Ford knew the procedure, but whether they got there in time…"

The two of them sat in silence.

TBC…

I already know how every bit of this story is going to be written so the whole thing will be posted within a week, 2 weeks at most.


	2. Chapter 2

Disclaimer: I don't own that crazy world of Stargate Atlantis

Note: Thanks for the reviews

**Atlantis **_(A few days later)_

John had been working non-stop the last few days trying to assemble a rescue mission in order to save Elizabeth and McKay. Ford was becoming worried about his CO, his friend. As he walked through the control room he saw John sat in Elizabeth's office, like he'd been the last two days. Ford walked over to Peter,

"As he said anything yet?"

Peter shook his head and looked towards the office

"I get the occasional 'Hello', but nothing other then that. He seems focused on planning a way to take the Genii home world."

Ford nodded

"Thanks, for keeping an eye on him"

Peter nodded and Ford walked into Elizabeth's office.

"Sir? John?"

John looked up. Tears were stinging his eyes.

"John"

Ford walked to his side. He wanted to be there for him, he just didn't know how to.

"We're going to save them. We're going to get them back."

Ford knew it was what John needed to hear, wanted to believe. It was just Ford didn't know whether he could believe it.

**Genii Home World**

Elizabeth opened her eyes. Once again blinded by the light that filled her small room. She was all alone; McKay had been taken away yesterday. Where they'd taken him or what they'd done to him, she didn't know. She moved into a sitting position, lying on the floor had been putting unwelcome pressure on her ribs. Elizabeth could feel tears forming in her eyes but she was determined not to show weakness or fear to her captures.

The door swung open, two guards came in and hauled her to her feet. They then marched her out of the room, along a corridor into another room where the pushed her onto a chair. Elizabeth was left alone for what seemed like hours until a familiar face walked into the room.

"Dr Weir, we meet again."

TBC…

Short chapter, already writing the next.


	3. Chapter 3

Disclaimer: I don't own Stargate Atlantis

Note: Thanks for the reviews

**Genii Home World**

Elizabeth stared into the eyes of her captor. She would not show weakness. She never showed weakness that was something that her parents forced into her. Especially her father, her father who never showed emotion. Even after her mother's suicide.  
Although even Elizabeth didn't show emotion when her mother died, that was because of her father. Now, for the first time in her life, she wanted to thank her father for the cold exterior he forced into her.

"Dr Weir, it is good to see you again."

"Where's Dr McKay?"

Kolya smirked

"He's being, _taken care of"_

"What does that mean?"

Kolya smirked again before walking over to her and took a strand of her hair, which he then placed behind her ear. Elizabeth drew back from his touch.

"I shall not harm you _Elizabeth_"

Elizabeth flinched when he said her name. Kolya only smirked more, he loved having a sense of power over her, the great leader of Atlantis was at his mercy, he wanted to savour that. The confident woman that he met on Atlantis was still there, although there was fear consuming her, Kolya knew she was trying to hide the fear from him.

"You shall achieve great things, if you let me show you the way."

Elizabeth looked up at him

"I don't want you to show me the way; I don't want you anywhere near me"

Kolya smirked; he loved her energy, her fire. He wanted her, wanted to show her what she could achieve, if she stayed with him.

"You'll change you mind _Elizabeth_, trust me."

He brushed his hand through her hair again before leaving the room.

Elizabeth waited until she was sure he was gone before she let a lone tear fall down her cheek. She was worried, not for herself, but for John, Rodney and everyone left on Atlantis. If they were still there. If they were still alive.

TBC…


	4. Chapter 4

Disclaimer: I do not own Stargate Atlantis.

Note: Thanks for the reviews

Spoiler to include 'The gift' because of the mention of a character.

**Genii Home World **_(Two months later)_

Elizabeth rolled onto her back and held her ribs.

"Please, no more"

Tears fell from her eyes. The Genii guard hit her with the stick once more before leaving.

Elizabeth rubbed her ribs as she sobbed quietly. The beatings were getting more and more regular. Elizabeth just hoped Rodney wasn't going through the same. She hadn't seen him since he was taken away; she was worried about him. No-one told her what had happened to him. She prayed for him. She prayed for John. For everyone on Atlantis.

Elizabeth pulled herself up and sat against the wall. Elizabeth was beginning to be able to tell the difference between the different weapons used on her. The different sticks had different functions. Some for pain, some for burning, some for bruising. She preferred the ones used for bruising, they didn't hurt as much. Elizabeth placed her head against the wall and sighed. The door opened again and Kolya walked in.

"Elizabeth"

She gotten used to him calling her that, she almost found it comforting, in a creepy, twisted way. He sat next to her.

"You said you wouldn't harm me."

Kolya laughed

"I have not."

Elizabeth shook her head.

"Where's Dr McKay?"

"He is okay"

"Good, can I see him?"

Kolya shook his head

"No"

Elizabeth brought her knees up to a chest and rested her chin on them ignoring the pain in her ribs.

"You are in pain."

"You are the one that ordered it."

"Cowen ordered it not me, I believe you are far too beautiful to harm."

Elizabeth shook her head and laughed

"Don't try that, it won't on me"

Kolya brushed away a piece of her hair.

"One day you will need me Elizabeth, one day you will come to me."

Kolya stood up and walked out of the room. She knew what Kolya was trying to do; she studied Stockholm syndrome, the threatening of life with random and short acts of kindness. She wouldn't let him get to her, she wouldn't. She couldn't. But everyday she knew that after he came she'd be unharmed until the next day under his order. The next day, it would happen again. Then again the next day. She didn't realise it, but she was going slightly mad.

**Atlantis **

The team consisting of John, Ford, Teyla and Stackhouse fell through the gate.

"Close the shield"

Peter closed the shield.

"Major what happened?"

Peter said as he came down the stairs.

"We mentioned the Genii."

Peter sighed as he looked at John; he looked tired, broken.

"Any sign of…Dr Weir or Dr McKay"

Peter saw the sad look in John's eyes, the looked that made him feel more sympathy for the Major.

"No"

Peter nodded and John made his way down to the infirmary. Followed by his team, excluding Ford who walked over to Peter

"He…he needs to talk to Heightmeyer, he's getting worse and I'm worried about him"

Peter nodded

"I'll arrange a meeting, but you convince him to go."

Ford nodded and followed his team down to the infirmary.

TBC…


	5. Chapter 5

Disclaimer: I don't own Stargate Atlantis.

Note: Spoiler alert to include 'The gift' purely because of the use of a character.

John sat in the office of resident psychologist Dr Kate Hightmeyer. She was sat across from him, clipboard in her hand.

"Major, we've been sat in here for over 30 minutes and you haven't said a word to me."

John just looked at her, responding with silence. Kate frowned. Aiden had been right, he was getting worse.

"John, please talk to me, that's what I'm here for."

John remained in silence and Kate wondered whether he was still with her, she leant forward and placed her hand on his arm. This got her a response, John looked at her before withdrawing his arm away from her.

"I'm sorry if I made you uncomfortable, I didn't mean too."

John looked at Kate. She stared into his eyes, she saw the coldness and hurt in them.

"John, please open up to me, I'm hear to listen. I know you're close to Dr's Weir and McKay and that this is difficult for you, but you have to talk about it"

John shifted slightly in his chair before looking at her again.

"I can't help but feel responsible…" Tears fell from John's eyes "…I'm the one who made an enemy of the Genii, I'm the reason Elizabeth and Rodney are missing, how do you expect me to feel?"

Kate looked at him sympathetically, she really did feel sorry for him, she knew some of the personal were blaming him and SGA-1. She didn't blame him, she knew Ford, Teyla and Peter didn't blame him. They were his friends and they'd be there for him for as long as he needed them.

**Genii Home world **_(5 Months later)_

Kolya found himself thrown to the ground by the woman who was now circling the room. Kolya got to his feet as the woman twisted the two sticks, she now held in her hands. Kolya grabbed a stick from the floor and circled the room himself. He charged at the women who bent backwards raising the sticks in a cross above her head so Kolya's stick connected with hers. She then lent forward and pushed him away and through his stick across the room. Kolya came at her again, but this time she dropped her sticks and pulled him into an embrace. Short, sweet, before releasing him.

"This is training time"

The woman sighed

"It is always time to train"

Kolya kissed her

"Do you want to be prepared, for when the time we shall seize Atlantis."

She sighed

"Of course, it is imperative that I be there to rescue my niece, my Sora and to punish she that killed my brother."

Kolya held her cheek

"Do not be set on revenge for your brother. Sora allowed herself to be captured by trying to seek revenge."

The door opened and a guard walked in

"Commander Kolya, sorry to interrupt Sir but Commander Cowen wishes to see you"

"I'll be right there."

He kissed the women one last time

"Go rest my love"

He walked out of the room, changed and went to Cowen's office. He knocked on the door before entering; Cowen looked up from the paper he was reading.

"Acastus, how our things with Dr Weir?"

Kolya couldn't be sure but something in Cowen's voice told him to be afraid for Elizabeth.

"She is fine, the programming worked. She does not remember a thing."

Cowen sat forward.

"And this…_relationship_ you have formed with her…"

"Is of part of her life with the Genii, it was imperative she hold some attachments to this world in order to forget her past."

Cowen glared at him

"That was why we used Sora and Tyrus as her attachments."

"Without Sora and Tyrus it was impossible, she'd never even met Tyrus and only spent a small amount of time with Sora. I did what I had too."

Cowen lent back,

"How can you be sure she is loyal to the Genii?"

"She as never said nor done anything that would suggest that she is not loyal. She believes she is Genii. That will come in valuable when we attack Atlantis. Her people will not harm her."

Cowen lent forward to Kolya

"Don't become too attached Kolya. If she becomes a liability to us. I will order her killed."

Kolya nodded

"I understand. Everything I do is to ensure she doesn't remember who she is."

Cowen nodded

"I would like you to pay a visit to Dr McKay, some of the scientists have been complaining about him. I would like you to remind McKay that we are in charge."

Kolya nodded

"Yes commander."

Kolya left the room and made his way to the lab where McKay was currently 'helping' the Genii prefect the atomic bombs.

When Kolya entered the lab, he heard a distinctive voice, which could have only come from one person.

"No, you see that's stupid. That'd never work. It would kill us all."

Kolya walked behind McKay and placed a hand on his shoulder.

"Dr McKay?"

McKay turned round and saw Kolya.

"Kolya, where's Elizabeth?"

Kolya smirked

"You know, you've been here for over seven months and every-time I see you, I get asked that same question, and like always I shall answer. _Elizabeth _is fine. She is being very co-operative."

"I want to see her."

Kolya shook his head; he was still smirking.

"That's impossible. I simply will not allow it."

Desperation entered McKay's voice.

"What have you done to her?"

"Nothing…" Kolya's smirked widened "…nothing that she hasn't consented too."

McKay felt sick. The smirk was telling McKay that Elizabeth was in trouble.

"I swear if you hurt her in any way…"

"You'll do what Dr McKay? You are in no position to do anything."

McKay sighed, he knew Kolya was right, there was nothing he could do that wouldn't cause more harm to Elizabeth.

"Just let me see her, let me see her and I'll do anything want me to. I just want to see she's okay."

Kolya thought for a moment. Letting McKay see Elizabeth could mean that the programming he'd worked so hard to prefect could be lost, or Elizabeth would remain under the programming and McKay would realise they'd done something to her. Kolya finally came up with a solution. But not letting McKay see Elizabeth could lead him to believe that she'd been killed at that point McKay would stop helping them in exchanged for her safety.

"You may see her, but you shall not communicate with her in any way. Do you understand?"

McKay nodded

"I understand."

Kolya smiled

"I shall set up a meeting for tomorrow."

Kolya walked out of the lab and, after changing, went up to the surface.

**Atlantis **

John sat in Elizabeth's office like he'd done for the last seven months, seven months without so much as a lead on where the Genii were keeping them, if they were even keeping them on their home world. Seven months without Elizabeth's warming smile, Hell he even missed the smile she gave him when she was trying to be pissed at him. John had one last shot at getting them back, they'd tried it before with no response from the Genii, maybe this time would be different.

John left the office and walked through the corridors of Atlantis. Wherever he went he received concerned looks and this time was no different, people watching him to see if he would break, people giving him judgemental looks. John was used to it, it had been happening for over seven months. However this time the looks he was receiving were bordering on scared and worried as he made his way to were Sora was being kept. In the last seven months, John had not visited Sora once, but now he was, and he had that glint in his eyes.

John walked into the area where they were keeping Sora. St Bates came up to John.

"Sir."

"Bates, ready the prisoner for transportation."

"Sir?"

Bates was confused over what he was being asked.

"Ready the prisoner for transportation. I'm contacting the Genii, I'm suggesting a trade. They get Sora we get Elizabeth and McKay."

Bates shook his head.

"Sir, I must ask you to reconsider. We've tried a trade before and they didn't get back to us."

"I know"

John walked away from Bates. Bates knew he was up to something, he only hoped it would save Weir and McKay and not harm them more.

TBC…


	6. Chapter 6

Disclaimer: I don't own Stargate Atlantis

Note: I've already written the last chapter, the only problem is I'm having trouble writing this chapter and the one after it. Please bear with me.

**Genii home world **_(The next day)_

Rodney awoke in a startle as he was yanked to his feet and dragged down the corridor of the Genii prison. Rodney was getting petty used to the 'wakeup calls' on this planet, they were never gentle about it. But today was different, today there were finally allowing him to see Elizabeth. He knew he couldn't talk to her but they had to be something he could do to communicate with her. A series of blinks, coughing the Morse code? Speaking in Russian? McKay quickly ran through the possibilities and decided that none of them would work perfectly but he had to know if she was alright.

* * *

Kolya brushed a piece of Elizabeths' hair away from her face as he watched her sleep. She was so peaceful when she was sleeping. Kolya had found himself becoming slowly enthralled by her over the months. The Elizabeth he had brought out was the woman she should be, this woman held a lot of power and potential and he wanted to be the one to bring it out. However, he saw similarities between this woman and Elizabeth Weir. Small similarities that no one other then him would realise. Elizabeth moved in closer to him. Kolya didn't love the woman laying next to him. He didn't love the woman she'd become. He felt more for Elizabeth Weir than Elizabeth Kolya. 

Elizabeth Weir was almost an innocent but Elizabeth Kolya was a ruthless killer. The only thing she was interested in was things, which would benefit her. She was interested in revenge. She stood for everything Elizabeth Weir despised. Kolya tried to tell himself he didn't love her. But it was becoming harder to deny his feelings.

She loved him though. Even though she was a killing machine she loved him, and that only scared Kolya further.

Elizabeth moved in closer to him.

"John"

It came in a murmur. Kolya was used to it. The only time she wasn't Elizabeth Kolya is when she was sleeping. Kolya had always been afraid that she'd remember her dreams, that she'd remember what had happened but she never did.

Kolya brushed his fingers through her hair.

He loved this time of the day. Before she woke up and went back to be a ruthless killing machine.

Elizabeths' eyes flickered open and Kolya smiled at her.

"You're finally awoke I see"

Elizabeth smiled at him and kissed him gently.

"We have things to do; she should have just woken me"

Kolya kissed her forehead.

"You look so peaceful when you sleep. I couldn't bear to wake you."

Elizabeth slid off the bed and walked over to the bathroom. Kolya had noticed how she seemed slightly different in the mornings, how she seemed more like Elizabeth Weir however nothing had ever come of it and he knew if Cowen found out she'd be in the nearest torture chamber within 5 minutes.

Elizabeth came out of the bathroom a few minutes later freshly showered. She got changed and walked over to the cabinet next to the bed, she looked at her reflection. She stared at herself deep in thought. Something was missing, something important and she couldn't figure out what. It was special to her, so knew that. She placed her hand on her bare neck. Remembering the feel of it. Cold against her skin only becoming warm because of her body heat.

"Acastus?"

Kolya was walking out of the bathroom when she called to him.

"Yes my dear"

She turned to him.

"Do I have a necklace, about so big…" She measure out the size with her fingers "…Silver, pointed oval shape?"

Kolya knew what she was talking about. The Genii had taken the necklace off her when she'd been locked up. Kolya shook his head.

"No, you've never had a necklace like that."

Elizabeth shook her head and smiled

"It's probably just something I dreamt of"

She left the bedroom. Kolya stood shocked for a moment. She'd never asked him anything that implied she remembered her old life, the only reason she would was if the programming was breaking down and if the programming was breaking down then meeting McKay could make her remember more. He could risk that.  
Kolya quickly dressed and left the bedroom.

* * *

McKay was waiting in a small room, with over a dozen armed guards. McKay really didn't think the guards were necessary, he wasn't going to try anything.  
McKay sat at the table. He didn't know what to expect. He didn't know what they'd done to Elizabeth but if they'd hurt her he'd make them regret it.

* * *

Kolya walked into the kitchen where Elizabeth was standing making breakfast. He was contemplating how to tell Elizabeth of the change of their plans. 

"Elizabeth, can we talk?"

Elizabeth turned to face him. Her face showed no emotion.

"Elizabeth, you will not be meeting with that Atlantis scientist today"

Elizabeth banged the cup she was holding on the table

"Why not? He was there when my brother was killed. He is just as guilty as Teyla Emmagan; he should be punished as well."

Kolya walked over to her.

"Your emotions are clouding your judgment. You want to kill him, fine. But first let him help us."

Elizabeth stared at Kolya before walking off abruptly.

**Atlantis**

John stood next to Peter.

"Dial the 'Gate'"

Peter began the dialling sequence. He, like several members of the crew, were unsure whether this plan would work or not. But he wasn't in the know about what the plan really was. Only John, Ford and a few privileged members of the military personal knew what was going to happen. John moved picked up the Genii communication device he'd picked up during the raid on Atlantis.

"Kolya, Cowen. This is Major Sheppard from Atlantis. I have a proposition for you. If you can hear me respond."

The radio crackled but no response came. John tried again.

"It's concerning Sora; we wish to make a trade. We give you Sora and the Wraith Data device and you give us Drs Weir and McKay"

The radio continued to crackle and John slammed it to the table, making Peter jump, Peter was about to shut down the Stargate when John stopped him

John moved to his own radio.

"Jumpers one, two and three execute"

Everyone was shocked as Jumper one appeared from the Jumper Bay. John walked down to the Jumper. Dr Beckett appeared from one corner of the room.

"Major Sheppard, what can I do for…?"

Beckett trailed off as John dragged up Jumper one's ramp and into the ship. Bates who had been watching the whole thing picked up his radio

"Major Sheppard, what's going on?"

"That's easy St. I'm bringing them home. Peter, you're in charge"

Peter looked down at the Jumper, which flew through the Stargate followed by another one. Peter didn't know the specifics of the plan, but he knew one thing. John Sheppard wouldn't rest until he succeeded. Peter dropped his head and picked up his own radio.

"Major Sheppard."

"Peter"

Peter closed his eyes.

"Be safe, and bring them home."

A moment of understanding passed between them.

"Will do"

Peter shut down the Stargate as the last of the cloaked Jumpers went through the 'Gate.

TBC…


	7. Chapter 7

Disclaimer: I don't own Stargate Atlantis

Note: Thanks for the reviews.

**Genii home world **

Cowen was slightly surprised when he heard Major John Sheppard on the radio. The last time Sheppard had contacted them had been months ago with the same offer. Cowen was not about to give up McKay. He'd fast tracked their bomb and they were only a few months away from completion. Weir on the other hand was a completely different matter. Cowen had never fully understood Kolyas' reasoning for programming Elizabeth into believing she was Genii. He knew that Kolya was willing to try and seize Atlantis again and he had told Cowen that with Elizabeth the members of Atlantis would not attack them even if she was programmed.

Cowen had heard it but he never quite believed it.

He'd seen Kolyas' attachment to Weir strengthen since the programming had taken hold. He was unsure of Kolyas' loyalty to the Genii. He was concerned with what Kolya would do if Weir regained her memory and discovered the truth.

Cowen thought about responding, thought about trading Weir for Sora just to get Kolya back to the man he was. But decided against it, maybe he could find a use for her.

**Jumper One (Genii home world)**

Beckett left his seat and walked over to John who was piloting the Puddle Jumper.

"You know this idea of yours is bloody barmy right?"

John nodded

"Yes, it's been brought to my attention. But I don't care. If this is the only way I'll get Elizabeth and Rodney back it's worth the risk."

Beckett sat back down. It was worth the risk and he knew that. He just hoped they didn't lose more good people in the process.

**Genii home world**

McKay was dragged from the warm intensity of the room to the cool surroundings outside the Genii village. For what reason? He didn't know. McKay waited until Kolya showed up.

"Do you like the surroundings McKay? I thought you'd like to see the outside world. It's been a while"

McKay walked over to him.

"I don't give a damn about the surroundings. Let me see Elizabeth"

Kolya smiled.

"She doesn't want to see you. She asked me to pass on her thanks for your concern and she wants you to keep helping us."

McKay shook his head.

"No she'd never say that. She'd never tell me too willingly to help you. What have you done to her?"

Kolya smirked.

"As I have said before, nothing she hasn't consented to."

Rage consumed McKay and he went to hit Kolya, but stopped short when a shot rang out through the valley. Kolya faltered back as a bullet ripped through his flesh. The guards standing around McKay fell as more shots rang out. McKay hit the floor as the shooting continued. After a moment, all went quiet.

"Rodney? McKay?"

McKay looked up.

"Sheppard."

John was standing over him.

"Are you hurt?"

McKay shook his head. Was he dreaming? John Sheppard was there. He held his hand out and helped McKay to his feet.

"Is that really you?"

John nodded, he couldn't resist the urge any longer and pulled him into a hug.

McKay hugged him back.

"Where's Elizabeth?"

McKay pulled himself out of John's hug and shook his head.

"I don't know. I haven't seen her in months."

John nodded his head.

"Where's the last place you saw her?"

McKay closed his eyes in an effort to remember.

"We were being held in a Genii cell. In the underground bunker."

John nodded.

"Then that's our first stop. Rodney I'm going to need you for this."

McKay nodded and John passed him a spare P-90.

"Just shot at what I tell you to."

McKay nodded as he held the P-90. It had been a while since he'd held any type of firearm but it was a bit like riding a bike. You never forget how to do it.

John began to order around the rest of the troops when a shot rang out.

"Take cover"

John, McKay and the Marines hid behind a fallen tree trunk as the shots continued to fire.

"Ford, who the hell is doing that?

"I don't know sir. We can't see the shooter."

John turned to his group.

"Make for the Jumper, I'll cover you. Go"

The three Marines and McKay made their way to the Jumper. Two shots rang out in quick succession. McKay fell to the ground. Two bullets had hit him in the back.

John moved from his position to his fallen friend, ordering the Marines to move.

"McKay, come on McKay move it."

John watched as McKays' face turned from pain to terror.

"Elizabeth?"

John was about to question him when he felt the cold, smooth metal of a Genii gun place itself on the side of his head.

"Drop the gun and turn around"

John knew the voice but it couldn't be. It was too cold, too hateful. John slowly put his gun down and turned around, gasping as he saw the woman standing in front of him.

"Elizabeth?"

She looked at him. Her eyes filled with hate. Her eyes were cold. It wasn't her and John knew that. But still he tried to break through

"Elizabeth, it's me, it's John"

Elizabeth stared at him, as if trying to place him. She was stopped when a Genii guard ran up to her.

"Ma'am. They have at least one ship that we've seen. Commander Cowen is on his way."

Elizabeth nodded. Her eyes scanned over the fallen Genii soldiers, until she spotted him.

"Acastus"

She moved over to him keeping her gun trained on John. She bent down beside him and placed a hand over his gunshot wound.

"Acastus"

John was stunned at what he was seeing. Elizabeth was showing concern for her capturer. John felt his world crashing down as she placed a kiss on Kolyas' forehead.

"What the hell?"

Elizabeth was clearly stunned by his outburst. She moved away from Kolya and walked back over to John.

"You will pay for his death." She looked down at McKay who was still bleeding on the floor "Just has he as paid for my brothers' death, just as Teyla Emmagan will pay."

John thought to himself. She had to be talking about Soras' father.

"Elizabeth, what's going on, this isn't you."

Elizabeth shook her head.

"If you know of my name you know of my reputation within the Genii. This is me, I assure you"

John tried to stand but was forced down by two guards.

"No. Your name is Elizabeth Weir. You're a diplomat from Earth. You're in charge of the Atlantis expedition. Come on Elizabeth remember"

Elizabeth shook her head, clearly amused.

"You are pitiful. My name is Elizabeth Kolya and you've just killed the man I love, you will not make me remember false things"

John shook his head.

"Elizabeth fight it."

John went though the memories in his mind trying to find something that would help her remember.

"You have a necklace. It's sliver, pointed oval shape. About so big" John measured with his fingers the size of the necklace.

Elizabeth looked at him, was she slowly remembering? John continued trying to remember things she'd told him, whenever she was lonely or even a little drunk.

"We grew up in Minnesota. You got a degree in politics when you were in University. When you were five you had a pet hamster that died it's name was…"

"…Sparky"

Elizabeth finished the sentence; Johns' hope increased and he continued

"After that you never had anymore pets because you couldn't handle death. Until you saw a dog that you instantly fell in love with."

Elizabeth placed her hands to her head; trying to remember? Forget? She wasn't sure which.

Ford came through on Johns' radio.

"Sir"

"Stay where you are Ford"

Elizabeths' head shot up

"Ford. Lt Aiden Ford, US Marine Corps. 25 years old."

John smiled. She had programmed the personal into her mind and that was breaking through Kolyas' programming.

The Genii guards started to advance on Elizabeth as the slowly realised what was happening. One of the pulled a gun on her.

"Elizabeth"

Elizabeths' head shot round to John as he rose up from his position and knocked her out of the bullets way.

"Jumpers One, Two and Three execute"

The three Jumpers appeared in the sky taking aim on the Genii soldiers. John shifted his gaze to Elizabeth who was huddled on the floor.

"Elizabeth."

He moved closer to her and she looked up at him tears in her eyes.

"John"

John wrapped his arms around her, trying to offer as much comfort as he could.

The jumpers dropped to ground level and began to disarm the Genii guards. Cowen and his guards were quickly disarmed as soon as they arrived on the scene. Cowen and the soldiers were rounded up and guarded as Beckett was called out of the Jumper to see to McKay.

"We're lucky whoever fired these shots has lousy aim."

Elizabeth spoke up for the first time in a while.

"That would be me. I shot him"

Elizabeth tensed as she said it. She'd always been against the use of guns and now she'd used one to shot her friend.

"Please tell me he'll be okay"

Beckett nodded

"He'll be fine, assuming we get him back to Atlantis. Soon"

John nodded and stood up helping Elizabeth to her feet. As the passed, the dead Genii soldiers she stopped for a moment looking at one. John came to her side and saw who she was looking at.

"Just walk away Elizabeth. Just walk away"

Elizabeth nodded her head slowly before getting on the Jumper not bothering to look back at the Genii soldiers or her past life.

As John walked passed Cowen, he stopped.

"I promise you. If I find anything wrong with her, I will come back and I will kill you."

Stackhouse emerged from the Jumper

"Sir?"

He nodded at John and John nodded back.

"As a gesture of goodwill between our two peoples I'll give you something in return for Elizabeth and Rodney"

Stackhouse walked down the ramp of the Jumper with Sora in tow. He walked her over to Cowen. John turned to Sora.

"I'm sure you'll be able to convince your people to stay away from mine"

Sora nodded

"Good"

John walked away from them.

"See Cowen, everything's worked out fine"

Cowen scowled at John who shrugged and entered the Jumper, he passed Elizabeth on his way over to the pilot seat and bent down in front of her.

"Hey, are you okay?"

She nodded slowly. John ran a thumb over one of her hands before he stood up and started up the Jumper.

During the flight back to the 'Gate, Ford came and sat beside his CO.

"Are you okay sir?"

John nodded and gave Ford a smile.

"I will be once we get back to Atlantis and Beckett gives them both a clean bill of health."

Ford looked over his shoulder at Elizabeth.

"Do you think she'll be okay?"

John sighed and dipped his head slightly

"I want to say yes, but she's been through a lot. We'll have to keep an eye on her for a while but I hope she'll be okay"

Ford nodded

"I know Sir. I hope she'll be okay too."

Ford looked at Elizabeth again. At how small she looked and he realised it might take much more than time to help her heal.

TBC…


	8. Chapter 8

Disclaimer: I don't own Stargate Atlantis

Note: Last Part.

Elizabeth had been back on Atlantis for just over a month and things seemed to be slowly getting back to normal. She was still not back in command, by her own decision, but was slowly catching up on mission reports. McKay had somehow found it in his heart to forgive her for shooting him and John was being extremely considerate and charming. This was all great, but it all felt false. She walked around all day with a smile on her face when all she wanted to do was breakdown. But she couldn't, the effort everyone, even Kavanagh, were putting in to help her transition back was astounding and she appreciated it, she really did. But she just wanted to forget any of it had ever happened. She tried to keep it within her but late one afternoon she just couldn't anymore. She walked to Kate Heightmeyers' office.

"Kate, do you have a moment?"

Kate smiled at her and gestured for her to enter. Elizabeth sat down opposite Kate.

"What can I do for you Elizabeth?"

Elizabeth dropped her head in her hands.

"I need to talk, about what happened. I know I said I didn't want to and that it wasn't necessary but truth be told I can't keep it in any longer."

Tears slowly fell from Elizabeths' eyes. She had over a dozen people on the base that would be more then happy to listen to her as she poured her heart out. John being the first among them but she didn't want them to know what was really happened to her. Kate, at the moment, was the only person she felt she could trust.

"Tell me how you feel Elizabeth"

Kate didn't exactly beat around the bush but this was the first time Elizabeth had wanted to discuss what had happened and she didn't want to lose that opportunity. Sure, she had talked to McKay about what he went through but she had a feeling that Elizabeths' ordeal had been so much worse.

"I feel used, violated, dirty. I can still feel that…_woman_…inside of me and I hate it. I hate that there is a woman like that inside me and I hate that Kolya was able to bring that out."

Elizabeth leaned back slightly

"I hate the fact that when I was her I did a number of questionable things without a second thought. I hate that Rodney as forgiven me so easily after I shot him, twice. The thing that scares be the most is that there is a woman inside of me that can actually do these things. I ask myself how I allowed it to happen and my thoughts always drift back to Kolya."

Kate sat forward slightly; this was getting interesting.

"There is a woman inside of me that can love a man like that. I wonder why the programming worked so well. Why I allowed myself to be manipulated"

Kate looked at Elizabeth sympathetically.

"You didn't allow yourself to be manipulated Elizabeth"

Elizabeth shook her head

"But I did. Some part of me must have wanted Kolya to programme me and it's terrifying that I wanted that."

Elizabeth closed her eyes and allowed her thoughts to drift, inside of her she found a dark place, the place where the woman she'd been still resided, as she looked into that woman she felt the feelings she had possessed for Kolya.

"She was in love with him. Kolya. She was in love with Kolya. Part of me was in love with the man that threatened to kill me. But somehow, I felt safe with him."

Kate noticed how Elizabeth had said 'I' instead of 'she'; Kate decided to push her.

"Did _you _love him Elizabeth?"

Elizabeths' head shot up.

"No, no never."

Kate observed Elizabeth. She was curious about what was happening inside her mind. She just had to reach for it.

"When Kolya was holding you as a prisoner, how did you feel about him?"

Elizabeth answered without thought

"I hated him. I still hate him."

Kate began to wonder if Kolya was the problem that Elizabeth was trying to rid herself of.

"How do you feel about yourself? Truthfully"

Elizabeth looked at her for a moment. Contemplating what to tell her but deciding that honesty was best.

"I'm ashamed of myself. I hate myself."

Kate was not convinced

"How do you feel about Major Sheppard?"

Elizabeth looked at her confused.

"What do you mean?"

"Well, he was the one who made an enemy of the Genii. He's the reason they came to seize Atlantis, he's the reason you were caught. Are you trying to tell me you don't feel any resentment against him?"

Elizabeth stood up abruptly.

"I have to go."

Elizabeth left the office and Kate began to wonder if she'd pushed things to far.

Elizabeth walked round the corridors of Atlantis thinking about what Kate had said. Her mind was overcome with thoughts. Did she blame John for what happened? Was that the reason she'd been avoiding him since she came back?

Elizabeth passed the control room and walked onto the balcony.

She lent against the railings and sighed, trying to rid herself of her thoughts.

How could she blame John? He'd saved her, risked his life trying to get her and Rodney back. Elizabeth sighed as the door to the balcony opened and someone stood beside her. She didn't need to look to see who it was. She already knew it was John.

"Are you okay Elizabeth?"

She turned to him and forced a smile

"Just thinking"

John lent against the railing.

"What about?"

Elizabeth sighed.

"I've just talked with Dr Heightmeyer. I needed to talk about what happened. I was confused and I think I still am."

John turned to her, obviously concerned.

"About what?"

Elizabeth considered whether she should tell him, after everything he done to save her, should she tell him that she _might _blame him?

"Heightmeyer asked me whether I blame you for what happened…"

Elizabeth turned to face him.

"…and I realised that I'd never actually thought about it."

John cut in, slightly agitated.

"Do _you _blame me?"

Elizabeth sighed

"No, I don't"

John looked back out onto the ocean.

"You don't sound too sure."

Elizabeth tried to cut in but John continued.

"When Kolya told me that you were dead I blamed myself for making an enemy of the Genii. When the Genii took you and Rodney I blamed myself again and when I said you on the Genii home world, holding that gun to my head I hated myself. I've carried around this guilt for over seven months and I don't want to feel that anymore."

Elizabeth brushed away a tear and forced him to turn to her. She brushed a hand down his cheek. John returned the action to her, gently brushing back her hair with his other hand.

"I don't blame you"

She whispered it quietly but enough for John to hear. He lowered his head and hovered his lips over hers. He waited for her to close the distance between them and she did, without hesitation.

Elizabeth pulled away a few moments later, remaining in his arms. She placed her head against his chest and he brushed his fingers through her hair. In this perfect moment Elizabeth considered what could have happened if John had saved her before Kolya dragged her through the Stargate and she had a feeling that she wouldn't have ended up in John's arms this soon if it had happened that way. Her Grandmother once told her that everything happens for a reason and maybe the reason she had taken by Kolya is so she could have this moment.

Fin


End file.
